Hi,
I guess officially the only way to parallelise bedpostx is to use SGE, but I
got it to process multiple slices simultaneously on a single machine by
making a few modifications to the bedpostx and fsl_sub scripts. This is on
Linux, but I don't see why it wouldn't work on another platform, so if you
are interested I can send you the diffs so you can try it out.
Eelke
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Jones, Richard
Sent: 15 May 2008 14:56
To: [log in to unmask]
Subject: [FSL] Parallel bedpostx
We are running FSL 4.0.4 on a Mac Pro with a dual quad core (i.e. 8
processors) and would like to speed up the bedpostx processing by
running it on several processors in parallel. The "Parallelising
bedpost" link from the bedpostx documentation describes how to set a
number of environment variables; we did this, and verified that the
variables had the desired values, but when we ran bedpostx it only ran
on a single processor. When looking elsewhere in the FSL documentation
it mentions using a Sun Grid Engine (SGE) for running a number of FSL
tasks (including bedpost), so does bedpostx require the SGE to be
installed or does it use a different mechanism for doing the parallel
processing? Also, has anyone has managed to bedpostx to run in parallel
on a Mac without using the SGE and if so did they make any changes other
than those described in the documentation?
Thanks,
Richard
--------------------------------------------
Richard Jones
Dept. of Radiology,
Children's Healthcare of Atlanta,
1001 Johnson Ferry Road,
Atlanta. GA 30342 USA.
Phone 404 785 5381
|